SRA

"Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species which sustains high revenue fisheries. This paper details the development of hundreds of SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted with a purely in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1536 GoldenGate assay. Although the rate of conversion of SNP candidates in the genotyping assay cannot be predicted in advance this approach has potential to maximise cost and time efficiencies as it avoids the expensive and time-consuming laboratory based SNP validation. Additionally, this approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is only based on the ability to design primers and the presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. This SNP panel represents a valuable multi-purpose resource for developing informative marker panels intended at discriminating populations, microarray development and for population genomic studies in the wild."